{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T15:19:16Z","timestamp":1793891956882,"version":"4.8.0"},"reference-count":81,"publisher":"Springer Science and Business Media LLC","issue":"8016","license":[{"start":{"date-parts":[[2024,5,29]],"date-time":"2024-05-29T00:00:00Z","timestamp":1716940800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,5,29]],"date-time":"2024-05-29T00:00:00Z","timestamp":1716940800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2024,6,13]]},"DOI":"10.1038\/s41586-024-07502-0","type":"journal-article","created":{"date-parts":[[2024,5,29]],"date-time":"2024-05-29T12:02:05Z","timestamp":1716984125000},"page":"429-436","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":150,"title":["A Gram-negative-selective antibiotic that spares the gut microbiome"],"prefix":"10.1038","volume":"630","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4129-2102","authenticated-orcid":false,"given":"Kristen A.","family":"Mu\u00f1oz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca J.","family":"Ulrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Archit K.","family":"Vasan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9206-1895","authenticated-orcid":false,"given":"Matt","family":"Sinclair","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6049-6904","authenticated-orcid":false,"given":"Po-Chao","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3506-4405","authenticated-orcid":false,"given":"Jessica R.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyang Yeon","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0338-6776","authenticated-orcid":false,"given":"Chien-Che","family":"Hung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7749-5844","authenticated-orcid":false,"given":"Christopher J.","family":"Fields","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8434-1010","authenticated-orcid":false,"given":"Emad","family":"Tajkhorshid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gee W.","family":"Lau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9018-3581","authenticated-orcid":false,"given":"Paul J.","family":"Hergenrother","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,29]]},"reference":[{"key":"7502_CR1","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41586-021-03986-2","volume":"599","author":"L Maier","year":"2021","unstructured":"Maier, L. et al. Unravelling the collateral damage of antibiotics on gut bacteria. Nature 599, 120\u2013124 (2021).","journal-title":"Nature"},{"key":"7502_CR2","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1056\/NEJMra1600266","volume":"375","author":"SV Lynch","year":"2016","unstructured":"Lynch, S. V. & Pedersen, O. The human intestinal microbiome in health and disease. New Eng. J. Med. 375, 2369\u20132379 (2016).","journal-title":"New Eng. J. Med."},{"key":"7502_CR3","doi-asserted-by":"publisher","first-page":"e00974","DOI":"10.1128\/mBio.00974-15","volume":"6","author":"AM Schubert","year":"2015","unstructured":"Schubert, A. M., Sinani, H. & Schloss, P. D. Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile. mBio 6, e00974 (2015).","journal-title":"mBio"},{"key":"7502_CR4","doi-asserted-by":"publisher","first-page":"S19","DOI":"10.1086\/521859","volume":"46","author":"RC Owens Jr.","year":"2008","unstructured":"Owens, R. C. Jr., Donskey, C. J., Gaynes, R. P., Loo, V. G. & Muto, C. A. Antimicrobial-associated risk factors for Clostridium difficile infection. Clin. Infect. Dis. 46, S19\u2013S31 (2008).","journal-title":"Clin. Infect. Dis."},{"key":"7502_CR5","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1016\/j.arcmed.2017.11.004","volume":"48","author":"T Iizumi","year":"2017","unstructured":"Iizumi, T., Battaglia, T., Ruiz, V. & Perez Perez, G. I. Gut microbiome and antibiotics. Arch. Med. Res. 48, 727\u2013734 (2017).","journal-title":"Arch. Med. Res."},{"key":"7502_CR6","first-page":"4303","volume":"600","author":"SSB Poon","year":"2022","unstructured":"Poon, S. S. B. et al. Neonatal antibiotics have long term sex-dependent effects on the enteric nervous system. J. Phys. 600, 4303\u20134323 (2022).","journal-title":"J. Phys."},{"key":"7502_CR7","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1159\/000443360","volume":"34","author":"K Lange","year":"2016","unstructured":"Lange, K., Buerger, M., Stallmach, A. & Bruns, T. Effects of antibiotics on gut microbiota. Digest. Dis. 34, 260\u2013268 (2016).","journal-title":"Digest. Dis."},{"key":"7502_CR8","doi-asserted-by":"publisher","first-page":"4547","DOI":"10.2147\/IDR.S281274","volume":"13","author":"S Gu","year":"2020","unstructured":"Gu, S. et al. Effect of the short-term use of fluoroquinolone and \u03b2-lactam antibiotics on mouse gut microbiota. Infect. Drug Resist. 13, 4547\u20134558 (2020).","journal-title":"Infect. Drug Resist."},{"key":"7502_CR9","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1093\/jac\/dkl420","volume":"58","author":"S Lofmark","year":"2006","unstructured":"Lofmark, S., Jernberg, C., Jansson, J. K. & Edlund, C. Clindamycin-induced enrichment and long-term persistence of resistant Bacteroides spp. and resistance genes. J. Antimicrob. Chemother. 58, 1160\u20131167 (2006).","journal-title":"J. Antimicrob. Chemother."},{"key":"7502_CR10","doi-asserted-by":"publisher","first-page":"191","DOI":"10.3390\/antibiotics9040191","volume":"9","author":"FB Hertz","year":"2020","unstructured":"Hertz, F. B. et al. Effects of antibiotics on the intestinal microbiota of mice. Antibiotics 9, 191 (2020).","journal-title":"Antibiotics"},{"key":"7502_CR11","doi-asserted-by":"publisher","first-page":"136","DOI":"10.3389\/fcimb.2012.00136","volume":"2","author":"JC Lagier","year":"2012","unstructured":"Lagier, J. C., Million, M., Hugon, P., Armougom, F. & Raoult, D. Human gut microbiota: repertoire and variations. Front. Cell Infect. Microbiol. 2, 136 (2012).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"7502_CR12","doi-asserted-by":"publisher","first-page":"161","DOI":"10.4103\/0972-5229.74179","volume":"14","author":"H Singh","year":"2010","unstructured":"Singh, H. Management with colistin. Ind. J. Crit. Care. Med. 14, 161\u2013162 (2010).","journal-title":"Ind. J. Crit. Care. Med."},{"key":"7502_CR13","doi-asserted-by":"publisher","first-page":"1333","DOI":"10.1086\/429323","volume":"40","author":"ME Falagas","year":"2005","unstructured":"Falagas, M. E. & Kasiakou, S. K. Colistin: the revival of polymyxins for the management of multidrug-resistant Gram-negative bacterial infections. Clin. Infect. Dis. 40, 1333\u20131341 (2005).","journal-title":"Clin. Infect. Dis."},{"key":"7502_CR14","doi-asserted-by":"publisher","first-page":"365","DOI":"10.5644\/ama2006-124.355","volume":"50","author":"M Chatzidimitriou","year":"2021","unstructured":"Chatzidimitriou, M. et al. mcr genes conferring colistin resistance in Enterobacterales; a five year overview. Acta Med. Acad. 50, 365\u2013371 (2021).","journal-title":"Acta Med. Acad."},{"key":"7502_CR15","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1086\/533452","volume":"197","author":"LB Rice","year":"2008","unstructured":"Rice, L. B. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J. Infect. Dis. 197, 1079\u20131081 (2008).","journal-title":"J. Infect. Dis."},{"key":"7502_CR16","doi-asserted-by":"publisher","first-page":"213","DOI":"10.3390\/antibiotics9050213","volume":"9","author":"PS Hoffman","year":"2020","unstructured":"Hoffman, P. S. Antibacterial discovery: 21st century challenges. Antibiotics 9, 213\u2013213 (2020).","journal-title":"Antibiotics"},{"key":"7502_CR17","doi-asserted-by":"publisher","first-page":"e02151","DOI":"10.1128\/AAC.02151-17","volume":"62","author":"NN Nickerson","year":"2018","unstructured":"Nickerson, N. N. et al. A novel inhibitor of the LolCDE ABC transporter essential for lipoprotein trafficking in Gram-negative bacteria. Antimicrob. Agents Chemother. 62, e02151\u201302117 (2018).","journal-title":"Antimicrob. Agents Chemother."},{"key":"7502_CR18","doi-asserted-by":"publisher","first-page":"6834","DOI":"10.1073\/pnas.1804670115","volume":"115","author":"G Zhang","year":"2018","unstructured":"Zhang, G. et al. Cell-based screen for discovering lipopolysaccharide biogenesis inhibitors. Proc. Natl Acad. Sci. USA 115, 6834\u20136839 (2018).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7502_CR19","doi-asserted-by":"publisher","first-page":"163","DOI":"10.3390\/antibiotics8040163","volume":"8","author":"KM Lehman","year":"2019","unstructured":"Lehman, K. M. & Grabowicz, M. Countering Gram-negative antibiotic resistance: recent progress in disrupting the outer membrane with novel therapeutics. Antibiotics 8, 163 (2019).","journal-title":"Antibiotics"},{"key":"7502_CR20","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1021\/jm2014748","volume":"55","author":"MF Brown","year":"2012","unstructured":"Brown, M. F. et al. Potent inhibitors of LpxC for the treatment of Gram-negative infections. J. Med. Chem. 55, 914\u2013923 (2012).","journal-title":"J. Med. Chem."},{"key":"7502_CR21","doi-asserted-by":"publisher","first-page":"1661","DOI":"10.1038\/s41564-022-01227-4","volume":"7","author":"RD Miller","year":"2022","unstructured":"Miller, R. D. et al. A novel antibiotic targeting BamA identified by a computational search. Nat. Microbiol. 7, 1661\u20131672 (2022).","journal-title":"Nat. Microbiol."},{"key":"7502_CR22","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1038\/s41586-019-1791-1","volume":"576","author":"Y Imai","year":"2019","unstructured":"Imai, Y. et al. A new antibiotic selectively kills Gram-negative pathogens. Nature 576, 459\u2013464 (2019).","journal-title":"Nature"},{"key":"7502_CR23","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1038\/s41586-018-0483-6","volume":"561","author":"PA Smith","year":"2018","unstructured":"Smith, P. A. et al. Optimized arylomycins are a new class of Gram-negative antibiotics. Nature 561, 189\u2013194 (2018).","journal-title":"Nature"},{"key":"7502_CR24","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/j.bbamcr.2004.02.005","volume":"1693","author":"H Tokuda","year":"2004","unstructured":"Tokuda, H. & Matsuyama, S.-I. Sorting of lipoproteins to the outer membrane in E. coli. Biochim. Biophys. Acta 1693, 5\u201313 (2004).","journal-title":"Biochim. Biophys. Acta"},{"key":"7502_CR25","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1038\/nchembio.221","volume":"5","author":"R Pathania","year":"2009","unstructured":"Pathania, R. et al. Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting. Nat. Chem. Biol. 5, 849\u2013856 (2009).","journal-title":"Nat. Chem. Biol."},{"key":"7502_CR26","doi-asserted-by":"publisher","first-page":"2426","DOI":"10.1016\/j.bmcl.2013.02.005","volume":"23","author":"CA Barker","year":"2013","unstructured":"Barker, C. A. et al. Degradation of MAC13243 and studies of the interaction of resulting thiourea compounds with the lipoprotein targeting chaperone LolA. Bioorg. Med. Chem. Lett. 23, 2426\u20132431 (2013).","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"7502_CR27","doi-asserted-by":"publisher","first-page":"e00246","DOI":"10.1128\/mBio.00246-11","volume":"2","author":"HH Hoang","year":"2011","unstructured":"Hoang, H. H. et al. Outer membrane targeting of Pseudomonas aeruginosa proteins shows variable dependence on the components of Bam and Lol machineries. mBio 2, e00246\u201300211 (2011).","journal-title":"mBio"},{"key":"7502_CR28","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1111\/j.1348-0421.2007.tb03906.x","volume":"51","author":"H Ito","year":"2007","unstructured":"Ito, H. et al. A new screening method to identify inhibitors of the Lol (localization of lipoproteins) system, a novel antibacterial target. Microbiol. Immun. 51, 263\u2013270 (2007).","journal-title":"Microbiol. Immun."},{"key":"7502_CR29","doi-asserted-by":"publisher","first-page":"1726","DOI":"10.1128\/JB.02552-14","volume":"197","author":"AS Nayar","year":"2015","unstructured":"Nayar, A. S. et al. Novel antibacterial targets and compounds revealed by a high-throughput cell wall reporter assay. J. Bacteriol. 197, 1726\u20131734 (2015).","journal-title":"J. Bacteriol."},{"key":"7502_CR30","doi-asserted-by":"publisher","first-page":"14352","DOI":"10.3390\/ijms232214352","volume":"23","author":"J Liu","year":"2022","unstructured":"Liu, J. et al. Natural inhibitors targeting the localization of lipoprotein system in Vibrio parahaemolyticus. Int. J. Mol. Sci. 23, 14352 (2022).","journal-title":"Int. J. Mol. Sci."},{"key":"7502_CR31","doi-asserted-by":"publisher","first-page":"e0069523","DOI":"10.1128\/aac.00695-23","volume":"68","author":"EBM Breidenstein","year":"2024","unstructured":"Breidenstein, E. B. M. et al. SMT-738: a novel small-molecule inhibitor of bacterial lipoprotein transport targeting Enterobacteriaceae. Antimicrob. Agents Chemother. 68, e0069523 (2024).","journal-title":"Antimicrob. Agents Chemother."},{"key":"7502_CR32","doi-asserted-by":"publisher","first-page":"4769","DOI":"10.1073\/pnas.1702248114","volume":"114","author":"M Grabowicz","year":"2017","unstructured":"Grabowicz, M. & Silhavy, T. J. Redefining the essential trafficking pathway for outer membrane lipoproteins. Proc. Natl Acad. Sci. USA 114, 4769\u20134774 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7502_CR33","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/nature22308","volume":"545","author":"MF Richter","year":"2017","unstructured":"Richter, M. F. et al. Predictive compound accumulation rules yield a broad-spectrum antibiotic. Nature 545, 299\u2013304 (2017).","journal-title":"Nature"},{"key":"7502_CR34","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1111\/nyas.13598","volume":"1435","author":"MF Richter","year":"2019","unstructured":"Richter, M. F. & Hergenrother, P. J. The challenge of converting Gram-positive-only compounds into broad-spectrum antibiotics. Ann. NY Acad. Sci. 1435, 18\u201338 (2019).","journal-title":"Ann. NY Acad. Sci."},{"key":"7502_CR35","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1021\/acs.accounts.0c00895","volume":"54","author":"KA Munoz","year":"2021","unstructured":"Munoz, K. A. & Hergenrother, P. J. Facilitating compound entry as a means to discover antibiotics for Gram-negative bacteria. Acc. Chem. Res. 54, 1322\u20131333 (2021).","journal-title":"Acc. Chem. Res."},{"key":"7502_CR36","doi-asserted-by":"publisher","first-page":"1863","DOI":"10.1021\/acs.analchem.8b03586","volume":"91","author":"H Prochnow","year":"2019","unstructured":"Prochnow, H. et al. Subcellular quantification of uptake in Gram-negative bacteria. Anal. Chem. 91, 1863\u20131872 (2019).","journal-title":"Anal. Chem."},{"key":"7502_CR37","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1128\/CMR.00008-07","volume":"20","author":"HM Wexler","year":"2007","unstructured":"Wexler, H. M. Bacteroides: the good, the bad, and the nitty-gritty. Clin. Microbiol. Rev. 20, 593\u2013621 (2007).","journal-title":"Clin. Microbiol. Rev."},{"key":"7502_CR38","doi-asserted-by":"publisher","first-page":"16169","DOI":"10.1073\/pnas.1311066110","volume":"110","author":"P Nonejuie","year":"2013","unstructured":"Nonejuie, P., Burkart, M., Pogliano, K. & Pogliano, J. Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules. Proc. Natl Acad. Sci. USA 110, 16169\u201316174 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7502_CR39","doi-asserted-by":"publisher","unstructured":"Grabowicz, M. Lipoproteins and their trafficking to the outer membrane. EcoSal Plus 8, https:\/\/doi.org\/10.1128\/ecosalplus.ESP-0038-2018 (2019).","DOI":"10.1128\/ecosalplus.ESP-0038-2018"},{"key":"7502_CR40","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/s41594-021-00573-x","volume":"28","author":"X Tang","year":"2021","unstructured":"Tang, X. et al. Structural basis for bacterial lipoprotein relocation by the transporter LolCDE. Nat. Struct. Mol. Biol. 28, 347\u2013355 (2021).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"7502_CR41","doi-asserted-by":"publisher","first-page":"4687","DOI":"10.1038\/s41467-021-24965-1","volume":"12","author":"S Sharma","year":"2021","unstructured":"Sharma, S. et al. Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins. Nat. Commun. 12, 4687 (2021).","journal-title":"Nat. Commun."},{"key":"7502_CR42","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1128\/IAI.05496-11","volume":"80","author":"CG Buffie","year":"2012","unstructured":"Buffie, C. G. et al. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect. Immun. 80, 62\u201373 (2012).","journal-title":"Infect. Immun."},{"key":"7502_CR43","doi-asserted-by":"publisher","first-page":"e01238-20","DOI":"10.1128\/mSphere.01238-20","volume":"6","author":"NA Lesniak","year":"2021","unstructured":"Lesniak, N. A., Schubert, A. M., Sinani, H. & Schloss, P. D. Clearance of Clostridioides difficile colonization is associated with antibiotic-specific bacterial changes. mSphere 6, e01238-20 (2021).","journal-title":"mSphere"},{"key":"7502_CR44","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-023-08096-0","volume":"23","author":"P Feuerstadt","year":"2023","unstructured":"Feuerstadt, P., Theriault, N. & Tillotson, G. The burden of CDI in the United States: a multifactorial challenge. BMC Infect. Dis. 23, 132 (2023).","journal-title":"BMC Infect. Dis."},{"key":"7502_CR45","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1021\/acsinfecdis.0c00869","volume":"7","author":"M Garcia Chavez","year":"2021","unstructured":"Garcia Chavez, M. et al. Synthesis of fusidic acid derivatives yields a potent antibiotic with an improved resistance profile. ACS Infect. Dis. 7, 493\u2013505 (2021).","journal-title":"ACS Infect. Dis."},{"key":"7502_CR46","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1093\/jac\/dkp024","volume":"63","author":"C Oefner","year":"2009","unstructured":"Oefner, C. et al. Increased hydrophobic interactions of iclaprim with Staphylococcus aureus dihydrofolate reductase are responsible for the increase in affinity and antibacterial activity. J. Antimicrob. Chemother. 63, 687\u2013698 (2009).","journal-title":"J. Antimicrob. Chemother."},{"key":"7502_CR47","doi-asserted-by":"publisher","first-page":"e01987-17","DOI":"10.1128\/AAC.01987-17","volume":"62","author":"KP Purnapatre","year":"2018","unstructured":"Purnapatre, K. P. et al. In vitro and in vivo activities of DS86760016, a novel leucyl-tRNA synthetase inhibitor for Gram-negative pathogens. Antimicrob. Agents Chemother. 62, e01987-17 (2018).","journal-title":"Antimicrob. Agents Chemother."},{"key":"7502_CR48","doi-asserted-by":"publisher","first-page":"eadg3683","DOI":"10.1126\/sciadv.adg3683","volume":"9","author":"M Schuster","year":"2023","unstructured":"Schuster, M. et al. Peptidomimetic antibiotics disrupt the lipopolysaccharide transport bridge of drug-resistant Enterobacteriaceae. Sci. Adv. 9, eadg3683 (2023).","journal-title":"Sci. Adv."},{"key":"7502_CR49","doi-asserted-by":"publisher","first-page":"112757","DOI":"10.1016\/j.ejmech.2020.112757","volume":"208","author":"P Rana","year":"2020","unstructured":"Rana, P. et al. FabI (enoyl acyl carrier protein reductase)\u2014a potential broad spectrum therapeutic target and its inhibitors. Eur. J. Med. Chem. 208, 112757 (2020).","journal-title":"Eur. J. Med. Chem."},{"key":"7502_CR50","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1021\/acscentsci.2c00598","volume":"8","author":"EN Parker","year":"2022","unstructured":"Parker, E. N. et al. An iterative approach guides discovery of the FabI inhibitor fabimycin, a late-stage antibiotic candidate with in vivo efficacy against drug-resistant Gram-negative infections. ACS Cent. Sci. 8, 1145\u20131158 (2022).","journal-title":"ACS Cent. Sci."},{"key":"7502_CR51","doi-asserted-by":"publisher","first-page":"4264","DOI":"10.1128\/AAC.00535-16","volume":"60","author":"J Yao","year":"2016","unstructured":"Yao, J. et al. A pathogen-selective antibiotic minimizes disturbance to the microbiome. Antimicrob. Agents Chemother. 60, 4264\u20134273 (2016).","journal-title":"Antimicrob. Agents Chemother."},{"key":"7502_CR52","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1146\/annurev-micro-090816-093754","volume":"71","author":"A Konovalova","year":"2017","unstructured":"Konovalova, A., Kahne, D. E. & Silhavy, T. J. Outer membrane biogenesis. Annu. Rev. Microbiol. 71, 539\u2013556 (2017).","journal-title":"Annu. Rev. Microbiol."},{"key":"7502_CR53","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1038\/s41586-018-0083-5","volume":"557","author":"H Ho","year":"2018","unstructured":"Ho, H. et al. Structural basis for dual-mode inhibition of the ABC transporter MsbA. Nature 557, 196\u2013201 (2018).","journal-title":"Nature"},{"key":"7502_CR54","doi-asserted-by":"publisher","first-page":"6379","DOI":"10.1016\/j.bmc.2016.06.044","volume":"24","author":"LL Silver","year":"2016","unstructured":"Silver, L. L. A Gestalt approach to Gram-negative entry. Bioorg. Med. Chem. 24, 6379\u20136389 (2016).","journal-title":"Bioorg. Med. Chem."},{"key":"7502_CR55","doi-asserted-by":"publisher","first-page":"1205","DOI":"10.1016\/j.bbamem.2012.01.009","volume":"1818","author":"KR Pandit","year":"2012","unstructured":"Pandit, K. R. & Klauda, J. B. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. Biochim. Biophys. Acta 1818, 1205\u20131210 (2012).","journal-title":"Biochim. Biophys. Acta"},{"key":"7502_CR56","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926\u2013935 (1983).","journal-title":"J. Chem. Phys."},{"key":"7502_CR57","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1002\/jcc.20945","volume":"29","author":"S Jo","year":"2008","unstructured":"Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859\u20131865 (2008).","journal-title":"J. Comput. Chem."},{"key":"7502_CR58","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1021\/acs.jcim.1c01388","volume":"62","author":"G Licari","year":"2022","unstructured":"Licari, G., Dehghani-Ghahnaviyeh, S. & Tajkhorshid, E. Membrane Mixer: a toolkit for efficient shuffling of lipids in heterogeneous biological membranes. J. Chem. Inform. Model. 62, 986\u2013996 (2022).","journal-title":"J. Chem. Inform. Model."},{"key":"7502_CR59","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 27\u201338 (1996). 33-38.","journal-title":"J. Mol. Graph."},{"key":"7502_CR60","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott, O. & Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455\u2013461 (2010).","journal-title":"J. Comput. Chem."},{"key":"7502_CR61","doi-asserted-by":"publisher","first-page":"044130","DOI":"10.1063\/5.0014475","volume":"153","author":"JC Phillips","year":"2020","unstructured":"Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).","journal-title":"J. Chem. Phys."},{"key":"7502_CR62","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"JC Phillips","year":"2005","unstructured":"Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781\u20131802 (2005).","journal-title":"J. Comput. Chem."},{"key":"7502_CR63","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1021\/ct200723y","volume":"8","author":"K Hart","year":"2012","unstructured":"Hart, K. et al. Optimization of the CHARMM additive force field for DNA: improved treatment of the BI\/BII conformational equilibrium. J. Chem. Theor. Comput. 8, 348\u2013362 (2012).","journal-title":"J. Chem. Theor. Comput."},{"key":"7502_CR64","doi-asserted-by":"publisher","first-page":"7830","DOI":"10.1021\/jp101759q","volume":"114","author":"JB Klauda","year":"2010","unstructured":"Klauda, J. B. et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B 114, 7830\u20137843 (2010).","journal-title":"J. Phys. Chem. B"},{"key":"7502_CR65","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N\u00b7log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089\u201310092 (1993).","journal-title":"J. Chem. Phys."},{"key":"7502_CR66","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"JP Ryckaert","year":"1977","unstructured":"Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327\u2013341 (1977).","journal-title":"J. Comput. Phys."},{"key":"7502_CR67","doi-asserted-by":"publisher","first-page":"4177","DOI":"10.1063\/1.467468","volume":"101","author":"GJ Martyna","year":"1994","unstructured":"Martyna, G. J., Tobias, D. J. & Klein, M. L. Constant-pressure molecular-dynamics algorithms. J. Chem. Phys. 101, 4177\u20134189 (1994).","journal-title":"J. Chem. Phys."},{"key":"7502_CR68","doi-asserted-by":"publisher","first-page":"4613","DOI":"10.1063\/1.470648","volume":"103","author":"SE Feller","year":"1995","unstructured":"Feller, S. E., Zhang, Y. H., Pastor, R. W. & Brooks, B. R. Constant-pressure molecular-dynamics simulation\u2014the Langevin piston method. J. Chem. Phys. 103, 4613\u20134621 (1995).","journal-title":"J. Chem. Phys."},{"key":"7502_CR69","unstructured":"Andrews, S. Fast QC: a quality control tool for high throughput sequence data. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/ (2016)."},{"key":"7502_CR70","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Method 13, 581\u2013583 (2016).","journal-title":"Nat. Method"},{"key":"7502_CR71","doi-asserted-by":"publisher","first-page":"e32491","DOI":"10.1371\/journal.pone.0032491","volume":"7","author":"Y Lan","year":"2012","unstructured":"Lan, Y., Wang, Q., Cole, J. R. & Rosen, G. L. Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms. PLoS ONE 7, e32491 (2012).","journal-title":"PLoS ONE"},{"key":"7502_CR72","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590\u2013D596 (2013).","journal-title":"Nucleic Acids Res."},{"key":"7502_CR73","doi-asserted-by":"publisher","unstructured":"McLaren, M. R. Silva SSU taxonomic training data formatted for DADA2. Zenodo https:\/\/doi.org\/10.5281\/zenodo.3986799 (2020).","DOI":"10.5281\/zenodo.3986799"},{"key":"7502_CR74","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1186\/s12859-015-0749-z","volume":"16","author":"ES Wright","year":"2015","unstructured":"Wright, E. S. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics 16, 322 (2015).","journal-title":"BMC Bioinformatics"},{"key":"7502_CR75","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2\u2014approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).","journal-title":"PLoS ONE"},{"key":"7502_CR76","unstructured":"R: A Language and Environment for Statistical Computing, v. 4.2.1 (R Foundation for Statistical Computing, 2019)."},{"key":"7502_CR77","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).","journal-title":"PLoS ONE"},{"key":"7502_CR78","unstructured":"Oksanen, J. et al. vegan: Community ecology package. https:\/\/CRAN.R-project.org\/package=vegan (2017)."},{"key":"7502_CR79","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"7502_CR80","doi-asserted-by":"publisher","unstructured":"Holmes, J. HPCBio\/hergenrother-16S-mouse-2022Sept: Initial release. https:\/\/doi.org\/10.5281\/zenodo.10980656 (2024).","DOI":"10.5281\/zenodo.10980656"},{"key":"7502_CR81","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s41564-019-0604-5","volume":"5","author":"EN Parker","year":"2020","unstructured":"Parker, E. N. et al. Implementation of permeation rules leads to a FabI inhibitor with activity against Gram-negative pathogens. Nat. Microbiol. 5, 67\u201375 (2020).","journal-title":"Nat. Microbiol."}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07502-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07502-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07502-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T11:03:54Z","timestamp":1718967834000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07502-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,29]]},"references-count":81,"journal-issue":{"issue":"8016","published-print":{"date-parts":[[2024,6,13]]}},"alternative-id":["7502"],"URL":"https:\/\/doi.org\/10.1038\/s41586-024-07502-0","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,29]]},"assertion":[{"value":"7 April 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 May 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 May 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The University of Illinois has filed patents on compounds described in this Article on which K.A.M. and P.J.H. are named inventors.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}